---
title: "MAFDash"
output:
  flexdashboard::flex_dashboard:
    source_code: embed
    theme: yeti
    orientation: rows
    vertical_layout: scroll
params:
  maffile: NULL
  titletext: "MAF Dash"
  plot_list: NULL
---

```{r setup, include=FALSE}
library(plotly)
library(dplyr)
library(crosstalk)
library(flexdashboard)
library(DT)
library(htmltools)
library(bsplus)
library(knitr)
library(maftools)
library(canvasXpress)
library(ggbeeswarm)
library(ComplexHeatmap)

maf_file <- params$maffile
title_text <- params$titletext

all_plot_opts <- params$plot_list
if (is.null(all_plot_opts)) {
  all_plot_opts = list("summary_plot"=TRUE,
                       "burden"=TRUE,
                       "oncoplot"=TRUE,
                       "cooccurence"=TRUE,
                       # "other"="custom_image.pdf",
                       "heatmap"=TRUE
                       )
}
# maf_file <- "/Users/tandonm/Documents/my_tools/MAFdash/4/data/TCGA_THYM/mutect2/TCGA_THYM.mutect2.maf"
# title_text <- ""
# rsource_files <- list.files(path="~/Documents/my_tools/MAFdash/Rpackage/MAFDashRPackage/R",
#                             pattern="*.R", full.names = T)
# for (funcfile in rsource_files) {
#   source(funcfile)
# }

template_dir <- getwd()
options(knitr.duplicate.label = "allow")

maf <- NULL

```


```{r read-MAF-file, results="hide" }

maf_data <- maf_file
clinical_data <- NULL

if (!is.null(maf_file)) {
  if (class(maf_file)=="MAF") {
    maf_data <- rbind(maf_file@data, maf_file@maf.silent)
    clinical_data <- maf_file@clinical.data
  }
  maf <- read.maf(maf_data, clinicalData = clinical_data)
}

```

```{r make-summary-table}
summary_table_text=NULL
if (!is.null(maf)) {
  summ_template_name=file.path(template_dir, "summary_table.Rmd")
  summary_table_text <- knitr::knit_expand(summ_template_name)
}
```
`r paste(knitr::knit(text = paste(summary_table_text, collapse = '\n')))`

Row {.tabset .tabset-fade data-height=800}
-------------------------------------

``` {r make-plot-tabs }
# all_plot_opts = list("summary_plot"=TRUE,
#                      # "burden"=TRUE,
#                      # "oncoplot"=TRUE,
#                      # "cooccurence"=TRUE,
#                      # "heatmap"=TRUE,
#                      "other"="~/Documents/my_tools/MAFdash/Rpackage/testing/custom_image.pdf"
#                      )

out <- lapply(names(all_plot_opts), function(plotname) {
  plot_input <- all_plot_opts[[plotname]]
  if (is.logical(plot_input) && plot_input) {
    template_name=file.path(template_dir, paste0(plotname, ".Rmd"))
    if (file.exists(template_name)) {
      return_text <- knitr::knit_expand(template_name)
    }
  } else {
    tab_text <- paste0("\n### ", plotname)
    rchunk_text <- c("``` {r, out.width='100%', out.height='95%' }","```")
    plot_text <- "print('Image not found')"
    if (is.character(plot_input) && file.exists(plot_input)) {
      plot_text <- paste0("knitr::include_graphics(all_plot_opts[['",plotname,"']])")
    } else if (class(plot_input)[1] %in% c("gg","Heatmap")) {
      plot_text <- paste0("print(all_plot_opts[['",plotname,"']])")
    } else if (class(plot_input)[1] %in% c("plotly")) {
      plot_text <- paste0("all_plot_opts[['",plotname,"']]")
    }
    return_text <- paste(tab_text, rchunk_text[1], plot_text, rchunk_text[2], sep="\n",collapse="\n")
  }
  return(return_text)
  
})
```
`r paste(knitr::knit(text = paste(out, collapse = '\n')))`

-------------------------------------

```{r make-variant-table}
var_table_text=NULL
if (!is.null(maf)) {
  vartbl_template_name=file.path(template_dir, "variant_table.Rmd")
  var_table_text <- knitr::knit_expand(vartbl_template_name)
}
```
`r paste(knitr::knit(text = paste(var_table_text, collapse = '\n')))`